Kristen K Dang <kristen.dang at="" ...=""> writes: > I am trying to use the lumiR function from the lumi package to read in a BeadStudio output file, but I keep > getting the following error: > > > input_file = "sample_probe_profile.txt"; > > data = lumiR(input_file, lib = 'lumiHumanV1') > Error in mget(targetID, get(paste(lib, "TARGETID2NUID", sep = ""), mode = "environment"), : > invalid first argument > In addition: Warning message: > In formatC(as.numeric(id), width = width, flag = "0", format = "d") : > NAs introduced by coercion ... On further investigation, I find that it is not the lumiR function itself that is causing the errors. I can run lumiR like so with the following error messages: data = lumiR(input_file) Warning message: In addNuId2lumi(x.lumi, lib = lib) : Please provide the annotation file or lumi annotation library! The earlier error (below) comes when I do this: data = addNuId2lumi(data, lib = 'lumiHumanV1') Error in mget(targetID, get(paste(lib, "TARGETID2NUID", sep = ""), mode = "environment"), : invalid first argument In addition: Warning message: In formatC(as.numeric(id), width = width, flag = "0", format = "d") : NAs introduced by coercion I get a similar error, and a new one, when I do the following: addControlData2lumi("control_probe_profile.txt", data) [1] "Inputting the data ..." [1] "Adding nuID to the data ..." Error in data.frame(controlType = controlType, ProbeID = ProbeID, controlData) : arguments imply differing number of rows: 0, 784 In addition: Warning message: In addNuId2lumi(x.lumi, lib = lib) : Please provide the annotation file or lumi annotation library! So my questions that remain: What is the problem with the addNuID function? What am I doing wrong regarding use of the control information? If anyone has insight about the use of lumi, please let me know! I would be very grateful.